Make one solid from mesh built out of multiple squares by snapping to grid
Blender is not Minecraft. You don't add boxes.
The best way not deal with unnecessary geometry is not to create it in the first place.
It makes no sense to have a whole bunch of duplicated faces just to delete them later.
Start your project over, and this time create just the shapes you need, with no internal faces. It will take you less time than to fix the current model and set you on the correct path to learn modelling.